Sodium in PDB 2yig: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.12 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.417, 36.074, 95.206, 90.00, 131.49, 90.00
R / Rfree (%)	18.4 / 22.1

The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor (pdb code 2yig). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor, PDB code: 2yig:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:18.3 occ:1.00 O A:GLU205 2.4 13.6 1.0 OD2 A:ASP128 2.5 16.6 1.0 O A:ASP203 2.9 11.9 1.0 OD1 A:ASP203 2.9 12.7 1.0 CG A:ASP128 3.2 14.7 1.0 OD1 A:ASP128 3.3 16.1 1.0 O A:HOH485 3.4 24.7 1.0 C A:ASP203 3.6 10.8 1.0 C A:GLU205 3.7 11.9 1.0 OG1 A:THR126 3.9 9.4 1.0 CG A:ASP203 4.0 11.8 1.0 CA A:ASP203 4.1 9.7 1.0 CD1 A:TRP207 4.2 9.6 1.0 CA A:THR206 4.4 12.2 1.0 N A:GLU205 4.4 10.1 1.0 N A:THR206 4.5 11.6 1.0 CD A:PRO127 4.5 10.3 1.0 CB A:ASP203 4.5 11.5 1.0 CB A:ASP128 4.5 12.6 1.0 C A:ASP204 4.6 11.1 1.0 N A:ASP204 4.6 9.7 1.0 CA A:GLU205 4.7 10.2 1.0 N A:TRP207 4.7 11.1 1.0 CA A:ASP204 4.8 10.6 1.0 NE1 A:TRP207 4.8 8.8 1.0 OD2 A:ASP203 5.0 13.6 1.0

Sodium binding site 2 out of 3 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:26.4 occ:1.00 O A:HOH551 1.9 16.3 1.0 O A:HOH543 2.1 18.7 1.0 O A:HOH504 2.4 16.8 1.0 O A:HOH481 2.4 25.2 1.0 O A:HOH474 3.4 15.3 1.0 O A:ALA188 3.5 8.9 1.0 O A:HOH523 3.7 16.9 1.0 CE1 B:PHE107 4.4 19.5 1.0 CZ B:PHE107 4.4 21.4 1.0 ND1 A:HIS226 4.5 8.4 1.0 CG A:HIS226 4.5 7.9 1.0 CE1 A:HIS226 4.6 8.6 1.0 CD2 A:HIS226 4.7 7.8 1.0 C A:ALA188 4.7 8.7 1.0 NE2 A:HIS226 4.8 7.9 1.0 CD A:PRO190 4.9 11.4 1.0 CB A:HIS226 5.0 8.0 1.0

Sodium binding site 3 out of 3 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:17.3 occ:1.00 OD2 B:ASP128 2.5 15.6 1.0 O B:GLU205 2.6 13.2 1.0 OD1 B:ASP203 2.7 12.1 1.0 O B:ASP203 3.0 12.0 1.0 CG B:ASP128 3.3 15.1 1.0 OG1 B:THR126 3.6 11.3 1.0 OD1 B:ASP128 3.6 16.6 1.0 C B:ASP203 3.7 11.5 1.0 C B:GLU205 3.8 13.0 1.0 CG B:ASP203 3.8 11.4 1.0 CD1 B:TRP207 4.1 9.9 1.0 CA B:ASP203 4.1 10.7 1.0 CD B:PRO127 4.3 10.0 1.0 CA B:THR206 4.3 12.0 1.0 CB B:ASP203 4.5 11.2 1.0 N B:THR206 4.5 12.2 1.0 N B:GLU205 4.5 12.5 1.0 CB B:ASP128 4.5 13.9 1.0 NE1 B:TRP207 4.7 9.7 1.0 N B:TRP207 4.7 11.1 1.0 N B:ASP204 4.7 11.2 1.0 OD2 B:ASP203 4.8 11.4 1.0 CA B:GLU205 4.8 12.8 1.0 C B:ASP204 4.8 12.3 1.0 CB B:THR126 4.9 9.2 1.0 CG B:PRO127 4.9 10.9 1.0 CA B:ASP204 5.0 12.3 1.0

C.D.Savi, A.D.Morley, A.Ting, I.Nash, K.Karabelas, C.M.Wood, M.James, S.J.Norris, G.Karoutchi, N.Rankine, G.Hamlin, P.A.Macfaul, D.Ryan, S.V.Baker, D.Hargreaves, S.Gerhardt. Selective Non Zinc Binding Inhibitors of MMP13. Bioorg.Med.Chem.Lett. V. 21 4215 2011.
ISSN: ISSN 0960-894X
PubMed: 21669521
DOI: 10.1016/J.BMCL.2011.05.075